The caBIO 4.3.1 is the minor release with some enhancement in FreeStyleLM Search Summary page and introduction of the Entrez-Gene data.
Release History
Release |
Date |
---|---|
4.3.1 Data Refresh |
September 2010 |
4.3.1 Data Refresh |
May 2010 |
4.3.1 |
January 2010 |
4.3 |
July 2009 |
4.2 |
January 2009 |
4.1 |
May 2008 |
4.0 |
December 2007 |
New Features and Updates
1. Enhanced Display of FreestyleLM Search Results
To allow users to more readily find data of interest, the results for a FreestyleLM search from the Home Page are now organized into categories based on domain objects.
2. Inclusion of all Entrez Genes
caBIO now provides all human and mouse genes from Entrez Gene. For details, please see the caBIO Data Release Notes.
Documentation Index
- caBIO 4.3.1 Data Refresh Release Notes(September 2010)
- caBIO 4.3.1 Data Refresh Release Notes(May 2010)
- caBIO 4.3.1 Release Notes
- caBIO Javadocs Online (Download)
- caBIO 4.3.1 Technical Guide
- caBIO Object Model in HTML (Download EA model)
- caBIO Data Sources
caBIO Code Examples using Entrez As a Base Gene Model
The new Entrez Gene data will be available through the existing caBIO APIs. Below are coding examples demonstrating the query of gene information using DatabaseCrossReference.
1. Querying for a Entrez Gene (BRCA1) and Get Pathways
DatabaseCrossReference dbRef = new DatabaseCrossReference(); dbRef.setDataSourceName("Entrez"); // Entrez dbRef.setCrossReferenceId("672"); // Entrez Gene Id for BRCA1 List<DatabaseCrossReference> refList = new ArrayList<DatabaseCrossReference>(); refList.add(dbRef); Gene gene = new Gene(); gene.setDatabaseCrossReferenceCollection(refList); try { List<Gene> resultList = appService.search(Gene.class, gene); for (Gene g : resultList) { System.out.println("Symbol: " + g.getSymbol()); System.out.println("Name: " + g.getFullName()); System.out.println("Taxon: " + g.getTaxon().getScientificName()); Collection<Pathway> pathways = g.getPathwayCollection(); for(Pathway p : pathways) { System.out.println(" Pathway: " 18 + p.getName()+" ("+p.getSource()+")"); } } } catch {}
The following is the output:
Symbol: BRCA1 Name: Breast cancer 1, early onset Taxon: Hs Pathway: h_atmPathway (BioCarta) Pathway: h_atrbrcaPathway (BioCarta) Pathway: h_bard1Pathway (BioCarta) Pathway: h_carm-erPathway (BioCarta) Pathway: h_g2Pathway (BioCarta) Pathway: h_ATM_mediated_phosphorylation_of_repair_proteins (Reactome) Pathway: h_Recruitment_of_repair_and_signaling_proteins_to_double_strand_breaks (Reactome)
2. Querying for a Unigene Gene (BRCA1) and Get Pathways
DatabaseCrossReference dbRef = new DatabaseCrossReference(); dbRef.setDataSourceName("Unigene"); // Unigene dbRef.setCrossReferenceId("Hs.194143"); // Unigene Cluster Id for BRCA1 List<DatabaseCrossReference> refList = new ArrayList<DatabaseCrossReference>(); refList.add(dbRef); Gene gene = new Gene(); gene.setDatabaseCrossReferenceCollection(refList); try { List<Gene> resultList = appService.search(Gene.class, gene); for (Gene g : resultList) { System.out.println("Symbol: " + g.getSymbol()); System.out.println("Name: " + g.getFullName()); System.out.println("Taxon: " + g.getTaxon().getScientificName()); Collection<Pathway> pathways = g.getPathwayCollection(); for(Pathway p : pathways) { System.out.println(" Pathway: " + p.getName()+" ("+p.getSource()+")"); } } } catch {}
The output is same as in example 1) above.
Old Archive Releases
For caBIO Archive Releases, please follow the link here.